I believe, and correct me if I'm wrong, that CIHR is a bit different than NSERC. From what I gathered, you need a pretty strong GPA to get NSERC. For CIHR, not so much. While NSERC might still look at the whole package, I believe they put much more emphasis on your undergrad GPA. If you have a great research proposal/training environment and a project which is interesting with a problem that should be addressed, you're more likely to get CIHR. They also look at your and your supervisor's publications/conference presentations etc. So having publications will definitively help you but being creative in your application with also give you a boost.
I received CIHR as an undergrad - no pubs, but good training environment and an interesting project. I haven't yet applied for Master's but I plan on writing the application the same way. You've got to engage them in some way and convince them that your project is important as well as outline why this would be a benefit in the health care field. That's at least what I gathered.
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"Let me know when your whole life goes up in smoke. That means it's time for a promotion." So true.
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